Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1033 to 1082 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
517	metaxin 2. [source:swissprot;acc:o75431]	Divided	219.537	234.793	1.06949	
517	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Subtracted	248.463	234.095	14.368	
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Divided	250.858	234.563	1.06947	
518	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Subtracted	218.596	204.344	14.252	
519	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Subtracted	218.613	204.382	14.231	
519	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Divided	218.702	204.582	1.06902	
520	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Subtracted	223.356	209.149	14.207	
520	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	Divided	214.754	229.565	1.06897	
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	Divided	215.237	230.07	1.06891	
521	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Subtracted	218.702	204.582	14.12	
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Divided	222.893	208.523	1.06891	
522	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Subtracted	229.709	215.631	14.078	
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	Divided	215.237	230.07	1.06891	
523	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Subtracted	247.47	233.441	14.029	
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	Divided	215.237	230.07	1.06891	
524	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Subtracted	247.47	233.441	14.029	
525	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	Divided	215.237	230.07	1.06891	
525	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Subtracted	247.47	233.441	14.029	
526	histone h2b. [source:refseq;acc:nm_175055]	Subtracted	247.47	233.441	14.029	
526	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	Divided	250.538	234.401	1.06884	
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	Divided	248.56	232.579	1.06871	
527	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	Subtracted	247.47	233.441	14.029	
528	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Subtracted	247.47	233.441	14.029	
528	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	Divided	222.146	237.393	1.06864	
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Divided	251.653	235.506	1.06856	
529	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Subtracted	247.47	233.441	14.029	
530	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	Subtracted	247.47	233.441	14.029	
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Divided	227.483	212.994	1.06803	
531	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	Subtracted	247.47	233.441	14.029	
531	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Divided	223.356	209.149	1.06793	
532	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Subtracted	112	126	14	
532	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Divided	250.942	235.004	1.06782	
533	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	58	44	14	
533	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Divided	250.942	235.004	1.06782	
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Divided	250.942	235.004	1.06782	
534	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	58	44	14	
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	Divided	236.662	252.708	1.0678	
535	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Subtracted	112	126	14	
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Divided	242.531	227.136	1.06778	
536	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Subtracted	112	126	14	
537	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	10	24	14	
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Divided	229.803	215.301	1.06736	
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	Divided	237.627	253.604	1.06724	
538	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	58	44	14	
539	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Subtracted	112	126	14	
539	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Divided	236.964	252.86	1.06708	
540	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	58	44	14	
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Divided	222.156	208.201	1.06703	
541	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Divided	222.156	208.201	1.06703	
541	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Subtracted	112	126	14	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/